+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6230 | |||||||||
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Title | AML1-175 + TRiC + Ni-nano-gold | |||||||||
Map data | AML1-175 + TRiC + Ni-nano-gold | |||||||||
Sample |
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Keywords | eukaryotic chaperonin | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 26.0 Å | |||||||||
Authors | Roh SH / Kasembeli M / Montoya JG / Trnka M / Lau WC / Burlingame A / Chiu W / Tweardy DJ | |||||||||
Citation | Journal: Biophys J / Year: 2016 Title: Chaperonin TRiC/CCT Recognizes Fusion Oncoprotein AML1-ETO through Subunit-Specific Interactions. Authors: Soung-Hun Roh / Moses M Kasembeli / Jesús G Galaz-Montoya / Wah Chiu / David J Tweardy / Abstract: AML1-ETO is the translational product of a chimeric gene created by the stable chromosome translocation t (8;21)(q22;q22). It causes acute myeloid leukemia (AML) by dysregulating the expression of ...AML1-ETO is the translational product of a chimeric gene created by the stable chromosome translocation t (8;21)(q22;q22). It causes acute myeloid leukemia (AML) by dysregulating the expression of genes critical for myeloid cell development and differentiation and recently has been reported to bind multiple subunits of the mammalian cytosolic chaperonin TRiC (or CCT), primarily through its DNA binding domain (AML1-175). Through these interactions, TRiC plays an important role in the synthesis, folding, and activity of AML1-ETO. Using single-particle cryo-electron microscopy, we demonstrate here that a folding intermediate of AML1-ETO's DNA-binding domain (AML1-175) forms a stable complex with apo-TRiC. Our structure reveals that AML1-175 associates directly with a specific subset of TRiC subunits in the open conformation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6230.map.gz | 25.2 MB | EMDB map data format | |
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Header (meta data) | emd-6230-v30.xml emd-6230.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | 400_6230.gif 80_6230.gif | 43.9 KB 4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6230 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6230 | HTTPS FTP |
-Validation report
Summary document | emd_6230_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
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Full document | emd_6230_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_6230_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6230 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6230 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6230.map.gz / Format: CCP4 / Size: 28.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | AML1-175 + TRiC + Ni-nano-gold | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : AML1-175 + TRiC + Ni-nano-gold
Entire | Name: AML1-175 + TRiC + Ni-nano-gold |
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Components |
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-Supramolecule #1000: AML1-175 + TRiC + Ni-nano-gold
Supramolecule | Name: AML1-175 + TRiC + Ni-nano-gold / type: sample / ID: 1000 / Oligomeric state: 16 / Number unique components: 2 |
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Molecular weight | Theoretical: 1 MDa |
-Macromolecule #1: TCP-1 Ring Complex
Macromolecule | Name: TCP-1 Ring Complex / type: protein_or_peptide / ID: 1 / Name.synonym: TRiC, CCT Details: Ni-1.4 nanometer gold particles were applied to the AML1-175-TRiC complex. Oligomeric state: 16 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: HeLa |
Molecular weight | Theoretical: 1 MDa |
-Macromolecule #2: AML1-175
Macromolecule | Name: AML1-175 / type: protein_or_peptide / ID: 2 / Name.synonym: domain of AML1-ETO protein / Details: related to Acute Myeloid Leukemia / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.4 Details: 20 mM HEPES, pH 7.4, 5 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 2% glycerol, 1% PEG8000, 0.05% OG, 0.02% BSA, 2% MeOH, 60 mM imidazole |
Grid | Details: 200 mesh Quantifoil holey carbon grid (1.2/1.3), acetone-washed and glow-discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Instrument: LEICA EM GP / Method: Blot for 10 seconds from copper side of grid. |
-Electron microscopy
Microscope | JEOL 2010F |
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Date | Nov 24, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 2.17 µm / Number real images: 99 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 69124 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: particle-based |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: OTHER / Software - Name: EMAN2, Relion1.2 / Number images used: 8346 |